ArticleNucleic acids research2024
ATLAS: protein flexibility description from atomistic molecular dynamics simulations.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed.
- Biasing Conformational Sampling in AlphaFold 3 and Boltz-2 via Pair Representation Scaling.Journal of chemical information and modeling · 2026Article
- Which Metrics Best Capture Protein Structural Changes in Molecular Dynamics Simulations? Evaluating Score Combinations and Force-Field Effects.Journal of chemical information and modeling · 2026Article
- Dynamics-aware evolutionary profiling uncouples structural rigidity from functional motion to enable enhanced variant interpretation.Functional & integrative genomics · 2026Article
- ESMDynamic: Fast and accurate prediction of protein dynamic contact maps from single sequences.Nature communications · 2026Article
- PETIMOT: a novel framework for inferring protein motions from sparse data using SE(3)-equivariant graph neural networks.Acta crystallographica. Section D, Structural biology · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.Journal of chemical theory and computation · 2026Article
- Structure-aware artificial intelligence for next-generation drug discovery: from protein-ligand modeling to generative biomolecular design.Briefings in bioinformatics · 2026Review
- Inferring dynamic information from protein structures by Gaussian integrals and deep learning.Bioinformatics (Oxford, England) · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- A dataset of small protein conformational ensembles from all-atom molecular dynamics simulations.Scientific data · 2026Article
- AI-based methods for simulating, sampling, and predicting protein ensembles.Current opinion in structural biology · 2026Review
- DynamicDTA: Drug-Target Binding Affinity Prediction Using Dynamic Descriptors and Graph Representation.Interdisciplinary sciences, computational life sciences · 2026Article
- A Risk-Tiered Validation Framework for Artificial Intelligence in Drug Discovery: From Reproducibility to Clinical Translation.International journal of molecular sciences · 2026Review
- DPLM: Dynamics-aware Protein Language Model via contrastive learning between sequence and molecular dynamics simulation trajectory.bioRxiv : the preprint server for biology · 2026Article
- Fast prediction of protein flexibility.Bioinformatics (Oxford, England) · 2026Article
- MDCompress: better, faster compression of molecular dynamics simulation trajectories.Bioinformatics (Oxford, England) · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
- Assessing the Performance of BioEmu in Understanding Protein Dynamics.International journal of molecular sciences · 2026Article
- Discovery of novel natural compounds as PKCθ inhibitors: structure-based virtual screening and in vitro evaluation.Journal of computer-aided molecular design · 2026Article
- Artificial intelligence-enabled multi-scale virtual cell: perspective, challenges, and opportunities.Briefings in bioinformatics · 2026Review
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5 authors.
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Abstract
Dynamical behaviour is one of the most crucial protein characteristics. Despite the advances in the field of protein structure resolution and prediction, analysis and prediction of protein dynamic properties remains a major challenge, mostly due to the low accessibility of data and its diversity and heterogeneity. To address this issue, we present ATLAS, a database of standardised all-atom molecular dynamics simulations, accompanied by their analysis in the form of interactive diagrams and trajectory visualisation. ATLAS offers a large-scale view and valuable insights on protein dynamics for a large and representative set of proteins, by combining data obtained through molecular dynamics simulations with information extracted from experimental structures. Users can easily analyse dynamic properties of functional protein regions, such as domain limits (hinge positions) and residues involved in interaction with other biological molecules. Additionally, the database enables exploration of proteins with uncommon dynamic properties conditioned by their environment such as chameleon subsequences and Dual Personality Fragments. The ATLAS database is freely available at https://www.dsimb.inserm.fr/ATLAS.
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